I'd argue that given it's a superhero universe, an alignment of some sort is almost essential, at least eventually - not necessarily this season, since [@Eddie Brock] established The Avengers, but eventually. 

In terms of how it affects the way the game is played, though, there's nothing to say that anyone has to treat it like it's a major thing that affects our individual characters. I don't really see a need for the whole Hall Of Justice/Avengers Mansion type of team where they have a place to convene or something, I see it as more of an understanding made that if a major threat arises and the respective hero can't go at it alone, they can easily extend a line to another (singular) PC for planned interactions. MME's would really need to be the only time that multiple heroes would team up. 

If it's done that way, the chance of it being affected by PC's who drop out are lessened entirely, unless a plan is made well in advance. In which case, the player affected just has to scrap that planned interaction and do something else. But I definitely don't think forming a team necessarily means that team gameplay suddenly needs to become a thing. Infact, I've never understood that approach to these things. It seems unnecessarily complicated compared to just saying "____ is a member of the Justice League/Avengers/Titans/X-Men" and leave it at that.

[b]EDIT:[/b] Or, y'know. What [@Superboy] said better and in lesser words. :lol